There is a lack of a generic tool in acquiring spatiotemporal and comparative genomic copy number in-situ for universal co-culture microbial community. Furthermore, many methods are limited to 2-dimensional (2D) observations. However, cells are in fact 3-dimensional (3D) structures and exist in 3D microbial consortia.
Some essential microbial cellular and community information are missing by most Molecular fingerprinting techniques. Denaturing Gradient Gale Electrophoresis (DGGE)(Muyzer, Waal, & Uitierlinden, 1993)(US7560236B62), clone libraries(US20140228223A1), T-RFLP (Terminal Restriction Fragment Length Polymorphism) methods, flow cytometry, Comparative genomic hybridization (CGH)(Pinkel et al., 1998)(Francisco, Kallioniemi, Waldman, & Francisco, 2000), DNA sequencing, real time-PCR(Pecoraro, Zerulla, Lange, & Soppa, 2011), need to destroy community structure and/or cellular integrity therefore ignore important info. such as spatial locus of cells and their in situ genomic copy number. Fluorescent In-situ hybridization (FISH)(US005880473A, US006136540A) maintains the cellular integrity, but lacks the genomic copy number and demands major efforts in developing specific fluorescent markers, which allow for limited applications.
The present invention overcomes the problems outlined above that provides the spatiotemporal and comparative intracellular ploidy that represents the growth rate of the cell (Akkermans, Elsas, & Bruijn, 1996). The present invention allows to maintain intact cell structures while identify the genera of the cells in the mixed culture and their 3D locus and intercellular structure. The present invention provides information of the relative genome size of the microorganisms in the mixture compare to those of their pure culture standards. The present method also provides relative metabolic growth rate of the cells and the spatiotemporal change of the community through inferential comparative genomic copy number evaluation. The invention presented makes it possible to compare standards of pure cultures with the mixed cultures to evaluate the growth of the cells within the mixtures and gain 3D information of the microbial community.